Error(s) in re-building vignettes:
  ...
--- re-building ‘myTAI.Rmd’ using rmarkdown
--- finished re-building ‘myTAI.Rmd’

--- re-building ‘other-strata.Rmd’ using rmarkdown
--- finished re-building ‘other-strata.Rmd’

--- re-building ‘phylo-expression-object.Rmd’ using rmarkdown
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
--- finished re-building ‘phylo-expression-object.Rmd’

--- re-building ‘phylostratigraphy.Rmd’ using rmarkdown
--- finished re-building ‘phylostratigraphy.Rmd’

--- re-building ‘tai-breaker.Rmd’ using rmarkdown
--- finished re-building ‘tai-breaker.Rmd’

--- re-building ‘tai-gallery.Rmd’ using rmarkdown
--- finished re-building ‘tai-gallery.Rmd’

--- re-building ‘tai-stats.Rmd’ using rmarkdown
--- finished re-building ‘tai-stats.Rmd’

--- re-building ‘tai-transform.Rmd’ using rmarkdown
--- finished re-building ‘tai-transform.Rmd’

--- re-building ‘taxonomy.Rmd’ using rmarkdown

Quitting from taxonomy.Rmd:307-311 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.itis.gov]:
Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
---
Backtrace:
     ▆
  1. ├─global taxonomy(organism = "Arabidopsis", db = "itis", output = "children")
  2. │ ├─base::as.data.frame(taxize::children(organism, db = db)[[1]])
  3. │ ├─taxize::children(organism, db = db)
  4. │ └─taxize:::children.default(organism, db = db)
  5. │   └─taxize:::process_children_ids(...)
  6. │     └─eval(fxn)(input, ...)
  7. │       └─ritis::terms(sci_com[i], what = searchtype, ...)
  8. │         └─base::lapply(query, fun, wt = wt, raw = raw, ...)
  9. │           └─ritis (local) FUN(X[[i]], ...)
 10. │             └─ritis:::itis_GET(path, list(srchKey = x), wt, ...)
 11. │               └─cli$get(query = args)
 12. │                 └─private$make_request(rr, mock)
 13. │                   └─crul:::crul_fetch(opts)
 14. │                     └─curl::curl_fetch_memory(x$url$url, handle = x$url$handle)
 15. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'taxonomy.Rmd' failed with diagnostics:
Timeout was reached [www.itis.gov]:
Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
--- failed re-building ‘taxonomy.Rmd’

SUMMARY: processing the following file failed:
  ‘taxonomy.Rmd’

Error: Vignette re-building failed.
Execution halted